Update the SYNOPSIS of some of the adaptors so that the example uses the

registry and not get_XXXAdaptor() explicitly.

modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm

@@ -3,28 +3,29 @@
 
 =head1 SYNOPSIS
 
-    $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
-        -user   => 'root',
-        -dbname => 'pog',
-        -host   => 'caldy',
-        -driver => 'mysql'
-        );
+    $db =
+      Bio::EnsEMBL::DBSQL::DBAdaptor->new( -user   => 'root',
+                                           -dbname => 'pog',
+                                           -host   => 'caldy',
+                                           -driver => 'mysql' );
 
     $gene_adaptor = $db->get_GeneAdaptor();
 
-    $gene = $gene_adaptor()->fetch_by_stable_id($stable_id);
+    $gene = $gene_adaptor->fetch_by_stable_id($stable_id);
 
-    $slice = $db->get_SliceAdaptor()->fetch_by_chr_start_end('X', 1, 10000);
+    $slice =
+      $db->get_SliceAdaptor()->fetch_by_chr_start_end( 'X', 1, 10000 );
 
 =head1 DESCRIPTION
 
 
 Formerly this class provided database connectivity and a means to retrieve
 object adaptors.  This class is now provided for convenience and backwards
-compatibility, but delegates its connection responsibilities to the
+compatibility, and delegates its connection responsibilities to the
 DBConnection class (no longer inherited from) and its object adaptor
 retrieval to the static Bio::EnsEMBL::Registry.
 
+Please use Bio::EnsEMBL::Registry to retrieve object adaptors.
 
 =head1 CONTACT
 

modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm

@@ -14,13 +14,17 @@ MySQL Database queries to load and store external object references.
 
 =head1 SYNOPSIS
 
-$db_entry_adaptor = $db_adaptor->get_DBEntryAdaptor();
-$db_entry = $db_entry_adaptor->fetch_by_dbID($id);
+  $db_entry_adaptor =
+    $registry->get_adaptor( 'Human', 'Core', 'DBEntry' );
 
-my $gene = $db_adaptor->get_GeneAdaptor->fetch_by_stable_id('ENSG00000101367');
-@db_entries = @{$db_entry_adaptor->fetch_all_by_Gene($gene)};
-@gene_ids = $db_entry_adaptor->list_gene_ids_by_extids('BAB15482');
+  $db_entry = $db_entry_adaptor->fetch_by_dbID($id);
 
+  my $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' );
+
+  my $gene = $gene_adaptor->fetch_by_stable_id('ENSG00000101367');
+
+  @db_entries = @{ $db_entry_adaptor->fetch_all_by_Gene($gene) };
+  @gene_ids   = $db_entry_adaptor->list_gene_ids_by_extids('BAB15482');
 
 =head1 CONTACT
 

modules/Bio/EnsEMBL/DBSQL/DensityTypeAdaptor.pm

@@ -12,10 +12,12 @@ Bio::EnsEMBL::DBSQL::DensityTypeAdaptor
 
 =head1 SYNOPSIS
 
-my $density_type_adaptor = $database_adaptor->get_DensityTypeAdaptor();
-@density_types = @{$density_type_adaptor->fetch_all()};
+  my $density_type_adaptor =
+    $registry->get_adaptor( 'Human', 'Core', 'DensityType' );
 
-my $dt = $density_type_adaptor->fetch_by_dbID(12);
+  my @density_types = @{ $density_type_adaptor->fetch_all() };
+
+  my $dt = $density_type_adaptor->fetch_by_dbID(12);
 
 
 =head1 DESCRIPTION

modules/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm

@@ -11,11 +11,11 @@ Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor - Adaptor for DnaAlignFeatures
 
 =head1 SYNOPSIS
 
-    $dafa = $dbadaptor->get_DnaAlignFeatureAdaptor();
+  $dafa = $registry->get_adaptor( 'Human', 'Core', 'DnaAlignFeature' );
 
-    @features = @{$dafa->fetch_by_Slice($slice)};
+  my @features = @{ $dafa->fetch_by_Slice($slice) };
 
-    $dafa->store(@features);
+  $dafa->store(@features);
 
 =head1 DESCRIPTION
 

modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm

@@ -18,8 +18,9 @@ storage of exon objects
 
 =head1 SYNOPSIS
 
-  $exon_adaptor = $database_adaptor->get_ExonAdaptor();
-  $exon = $exon_adaptor->fetch_by_dbID($dbID);
+  my $exon_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Exon' );
+
+  my $exon = $exon_adaptor->fetch_by_dbID($dbID);
 
 =head1 DESCRIPTION
 

modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm

@@ -15,10 +15,13 @@
 
 =head1 SYNOPSIS
 
-  my $meta_container = $db_adaptor->get_MetaContainer();
+  my $meta_container =
+    $registry->get_adaptor( 'Human', 'Core', 'MetaContainer' );
+
   my $species = $meta_container->get_Species();
 
-  my @mapping_info = @{$meta_container->list_value_by_key('assembly.mapping')};
+  my @mapping_info =
+    @{ $meta_container->list_value_by_key('assembly.mapping') };
 
 =head1 DESCRIPTION
 

modules/Bio/EnsEMBL/DBSQL/MiscSetAdaptor.pm

@@ -15,14 +15,12 @@ Bio::EnsEMBL::MiscSet objects.
 
 =head1 SYNOPSIS
 
-  #$db is a Bio::EnsEMBL::DBSQL::DBAdaptor object:
-  $msa = $db->get_MiscSetAdaptor();
+  my $msa = $registry->get_adaptor( 'Human', 'Core', 'MiscSet' );
 
-  $misc_set = $msa->fetch_by_dbID(1234);
+  my $misc_set = $msa->fetch_by_dbID(1234);
 
   $misc_set = $msa->fetch_by_code('clone');
 
-
 =head1 DESCRIPTION
 
 This class provides database interactivity for MiscSet objects.  MiscSets

modules/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm

@@ -14,12 +14,12 @@ Adaptor for ProteinAlignFeatures
 
 =head1 SYNOPSIS
 
-    $pafa = $dbadaptor->get_ProteinAlignFeatureAdaptor();
+  $pafa =
+    $registry->get_adaptor( 'Human', 'Core', 'ProteinAlignFeature' );
 
-    my @features = @{$pafa->fetch_all_by_Slice($slice)};
-
-    $pafa->store(@features);
+  my @features = @{ $pafa->fetch_all_by_Slice($slice) };
 
+  $pafa->store(@features);
 
 =head1 DESCRIPTION
 

modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm

@@ -13,8 +13,10 @@ Bio::EnsEMBL::DBSQL::SequenceAdaptor - produce sequence strings from locations
 
 =head1 SYNOPSIS
 
-$seq_adptr = $database_adaptor->get_SequenceAdaptor();
-$dna = ${$seq_adptr->fetch_by_Slice_start_end_strand($slice, 1, 1000, -1);}
+  my $sa = $registry->get_adaptor( 'Human', 'Core', 'Sequence' );
+
+  my $dna =
+    ${ $sa->fetch_by_Slice_start_end_strand( $slice, 1, 1000, -1 ) };
 
 =head1 DESCRIPTION
 

modules/Bio/EnsEMBL/DBSQL/StatementHandle.pm

@@ -106,7 +106,7 @@ sub DESTROY {
 # Comment out this "__END__" for printing out handy debug information
 # (every query if you want).
 
-__END__
+#__END__
 
 # To stop caching messing up your timings, try doing the following on
 # any adapter:

modules/Bio/EnsEMBL/DBSQL/SupportingFeatureAdaptor.pm

@@ -12,11 +12,10 @@ features from the database.
 
 =head1 SYNOPSIS
 
-  $supporting_feature_adaptor =
-    $database_adaptor->get_SupportingFeatureAdaptor();
+  my $sfa =
+    $registry->get_adaptor( 'Human', 'Core', 'SupportingFeature' );
 
-  @supporting_feats =
-    @{ $supporting_feat_adaptor->fetch_all_by_Exon($exon) };
+  my @supporting_feats = @{ $sfa->fetch_all_by_Exon($exon) };
 
 =head1 CONTACT
 

modules/Bio/EnsEMBL/DBSQL/UnconventionalTranscriptAssociationAdaptor.pm

@@ -13,9 +13,10 @@ Bio::EnsEMBL::DBSQL::UnconventionalTranscriptAssociationAdaptor
 
 =head1 SYNOPSIS
 
-$utaa = $database_adaptor->get_UnconventionalTranscriptAssociationAdaptor();
+  $utaa = $registry->get_adaptor( 'Human', 'Core',
+                                'UnconventionalTranscriptAssociation' );
 
-my $uta = $utaa->fetch_all_by_type('antisense');
+  my $uta = $utaa->fetch_all_by_type('antisense');
 
 =head1 DESCRIPTION
 
@@ -175,6 +176,7 @@ sub fetch_all_by_transcript {
   Caller     : general
   Status     : At Risk
              : under development
+
 =cut
 
 sub store {